The invention discloses a water-soluble organic fertilizer for pitaya, and a preparation method thereof, and belongs to the technical field of agricultural planting, wherein the water-soluble organic fertilizer comprises, by weight, 0.5-0.8 part of fosamine-ammonium, 0.5-1.3 parts of daminozide, 10-20 parts of oxalic acid, 10-20 parts of citric acid, 10-20 parts of selenate, 20-30 parts of a water-soluble organic matter, 30-50 parts of pigeon manure, 20-30 parts of sheep manure, 10-20 parts of tobacco powder, 15-30 parts of mushroom residue, 10-20 parts of sesbania cannabina, 10-20 parts of alfalfa, 10-20 parts of astragalus sinicus l, 1-3 parts of a trace element fertilizer, 3-6 parts of ash formed by firing of rice hull, 0.5-1 part of fermentation bacteria, and 30-50 parts of water. The water-soluble organic fertilizer of the present invention has advantages of simple preparation method, reasonable component ratio and high nutrient content, can promote the growth and development, the high yield and the high quality of pitaya, and is suitable for large-scale promotion and use.